Methods in Ecology and Evolution

Article	Citations
occupancyTuts: Occupancy modelling tutorials with RPresence	658
Cover Picture and Issue Information	392
Cover Picture and Issue Information	373
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FlywayNet: A hidden semi‐Markov model for inferring the structure of migratory bird networks from count data	182
Revticulate: An R framework for interaction with RevBayes	165
A network theoretic method for the basic reproductive number for infectious diseases	135
Assimilating ecological theory with empiricism: Using constrained generalized additive models to enhance survival analyses	132
AF‐vapeR: A multivariate genome scan for detecting parallel evolution using allele frequency change vectors	122
Nearest neighbour distance matching Leave‐One‐Out Cross‐Validation for map validation	112
poems: R package for simulating species' range dynamics using pattern‐oriented validation	107
BATScan: A radar classification tool reveals large‐scale bat migration patterns	107
ECOGEN: Bird sounds generation using deep learning	93
OCCUR Shiny application: A user‐friendly guide for curating species occurrence records	91
Empirical dynamic programming for model‐free ecosystem‐based management	89
plantR: An R package and workflow for managing species records from biological collections	80
Integrated community occupancy models: A framework to assess occurrence and biodiversity dynamics using multiple data sources	77
Cover Picture and Issue Information	76
Using cloud radar to investigate the effect of rainfall on migratory insect flight	75
Nighthawk: Acoustic monitoring of nocturnal bird migration in the Americas	73
Exploring congruent diversification histories with flexibility and parsimony	72
How to get the most out of phylogenetic imputation without abusing it	69
A new centrality index designed for multilayer networks	66
Exploring noise, degeneracy and determinism in biological networks with the einet package	65

Incidence‐data‐based species richness estimation via a Beta‐Binomial model	64
Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution	64
Using identity calls to detect structure in acoustic datasets	63
Filtering heart rates using data densities: The boxfilter R package	63
The Flora Incognita app – Interactive plant species identification	62
Cover Picture and Issue Information	59
An open future for MEE	58
Integrated movement models for individual tracking and species distribution data	58
Gone with the wind: Inferring bird migration with light‐level geolocation, wind and activity measurements	56
Going beyond richness: Modelling the BEF relationship using species identity, evenness, richness and species interactions via the DImodels R package	56
EcoEnsemble: A general framework for combining ecosystem models in R	55
A general framework for jointly modelling thermal and hydric constraints on developing eggs	55
Towards biologically realistic estimates of home range and spatial exposure for colonial animals	55
Long‐term automated visual monitoring of Antarctic benthic fauna	53
Navigating through space and time: A methodological approach to quantify spatiotemporal connectivity using stream flow data as a case study	53
Moving‐resting process with measurement error in animal movement modeling	53
A systematic method for hypothesis synthesis and conceptual model development	52
MoonShine: A software‐hardware system for simulating moonlight ground illuminance and re‐creating artificial moonlight cycles in a laboratory environment	52
treetop: A Shiny‐based application and R package for extracting forest information from LiDAR data for ecologists and conservationists	51
Scalable semantic 3D mapping of coral reefs with deep learning	50
Continuous on‐board behaviour classification using accelerometry: A case study with a new GPS‐3G‐Bluetooth system in Pacific black ducks	50
A 3D modelling approach to measuring structural characteristics of bird nest interiors	48
Individual‐based simulations of genome evolution with ancestry: The GenomeAdmixR R package	47
Chronospaces: An R package for the statistical exploration of divergence times promotes the assessment of methodological sensitivity	47
Multi‐trait point pattern reconstruction of plant ecosystems	46
Benchmarking imputation methods for categorical biological data	46
Classifying the activity states of small vertebrates using automated VHF telemetry	45
Plant biodiversity assessment through soil eDNA reflects temporal and local diversity	44
Dynamic visualisation of million‐tip trees: The OneZoom project	42
Measuring reflectance of tiny organisms: The promise of species level biocrust remote sensing	39
Overall dynamic body acceleration measures activity differently on large versus small aquatic animals	38
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Introducing recurrent event analyses to assess species interactions based on camera‐trap data: A comparison with time‐to‐first‐event approaches	38
Corrigendum	37
Cover Picture and Issue Information	37
Retrodiction of forest demography: Backward simulation with reverse matrix models	36
treats: A modular R package for simulating trees and traits	36
Parasitic flowering plant collections embody the extended specimen	36
RFIDeep: Unfolding the potential of deep learning for radio‐frequency identification	36
Handbook of protocols for standardized measurements of floral traits for pollinators in temperate communities	34
Automated retrieval of information on threatened species from online sources using machine learning	33
Building ecological networks with local ecological knowledge in hyper‐diverse and logistically challenging ecosystems	33
Detecting and reducing heterogeneity of error in acoustic classification	32
Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves	32
Automated identification of diverse Neotropical pollen samples using convolutional neural networks	31
RevGadgets: An R package for visualizing Bayesian phylogenetic analyses from RevBayes	31
A Double machine learning trend model for citizen science data	30
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Food web reconstruction through phylogenetic transfer of low‐rank network representation	29
Sourcing high tissue quality brains from deceased wild primates with known socio‐ecology	28

Measuring understorey vegetation structure using a novel mixed‐reality device	28
PicoCam: High‐resolution 3D imaging of live animals and preserved specimens	28
PleistoDist: A toolbox for visualising and quantifying the effects of Pleistocene sea‐level change on island archipelagos	28
Using standardized fish‐specific autonomous reef monitoring structures (FARMS) to quantify cryptobenthic fish communities	27
An aquaria set‐up for long‐term, multiple‐stressor research in marine organisms	27
When to monitor or control: Informed invasive species management using a partially observable Markov decision process (POMDP) framework	27
The Wayqecha Amazon Cloud Curtain Ecosystem Experiment: A new experimental method to manipulate fog water inputs in terrestrial systems	27
qad: An R‐package to detect asymmetric and directed dependence in bivariate samples	27
Linear polyacrylamide is highly efficient in precipitating and purifying environmental and ancient DNA	27
Using causal diagrams and superpopulation models to correct geographic biases in biodiversity monitoring data	27
Existing and emerging uses of drones in restoration ecology	26
Unbiased population heterozygosity estimates from genome‐wide sequence data	26
Accelerating advances in landscape connectivity modelling with the ConScape library	26
The r package enerscape: A general energy landscape framework for terrestrial movement ecology	26
Issues in calibrating models with multiple unbalanced constraints: the significance of systematic model and data errors	26
TreeCompR: Tree competition indices for inventory data and 3D point clouds	25
Hidden Markov models: Pitfalls and opportunities in ecology	25
Use of amino acid isotope analysis to investigate capital versus income breeding strategies in migratory avian species	25
Metabolic proxy for cephalopods: Stable carbon isotope values recorded in different biogenic carbonates	25
A cost‐effective method to passively sample communities at the forest canopy–aerosphere interface	25
Integrated SDM database: Enhancing the relevance and utility of species distribution models in conservation management	25
Tracking the frequency of phytoplankton clonal lineages using multispectral image flow cytometry and neural networks	25
A wireless, remotely operable and easily customizable robotic flower system	25
Methods for testing publication bias in ecological and evolutionary meta‐analyses	25
Generating spatially realistic environmental null models with the shift‐&‐rotate approach helps evaluate false positives in species distribution modelling	25
In situ estimation of active dispersal abilities in reef fish early life stages using tracking technologies	24
Optimising sampling designs for habitat fragmentation studies	24
Writing a massively multi‐authored paper: Overcoming barriers to meaningful authorship for all	24
TaxoNERD: Deep neural models for the recognition of taxonomic entities in the ecological and evolutionary literature	24
Detecting seasonal episodic‐like spatio‐temporal memory patterns using animal movement modelling	24
OpenSoundscape: An open‐source bioacoustics analysis package for Python	23
A process approach to quality management doublesNEONsensor data quality	23
The CV is dead, long live the CV!	23
The power of forecasts to advance ecological theory	23
An automatic classifier of bat sonotypes around the world	23
Estimating process‐based model parameters from species distribution data using the evolutionary algorithm CMA‐ES	22
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A framework to model a web of linkage disequilibria for natural allotetraploid populations	22
The Movebank system for studying global animal movement and demography	22
Limits to ecological forecasting: Estimating uncertainty for critical transitions with deep learning	22
tidysdm: Leveraging the flexibility of tidymodels for species distribution modelling in R	22
Evo‐Scope: Fully automated assessment of correlated evolution on phylogenetic trees	22
Temporal design for aquatic organismal sampling across the National Ecological Observatory Network	22
NAPS: Integrating pose estimation and tag‐based tracking	22
Cover Picture and Issue Information	21
Estimating species misclassification with occupancy dynamics and encounter rates: A semi‐supervised, individual‐level approach	21
The uniform AUC: Dealing with the representativeness effect in presence–absence models	21
sabinaNSDM: An R package for spatially nested hierarchical species distribution modelling	21
poolHelper: An R package to help in designing Pool‐Seq studies	21
Monitoring fast‐moving animals—Building a customized camera system and evaluation toolset	21
How to generate accurate continuous thermal regimes from sparse but regular temperature measurements	21
Synthesizing forecasts to inform decision‐making and advance ecological theory	20
ipsecr: An R package for awkward spatial capture–recapture data	20
Precise tactile stimulation of worker ants by a robotic manipulator reveals that individual responses are density‐ and context‐dependent	20
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soundscape_IR: A source separation toolbox for exploring acoustic diversity in soundscapes	19
Scaling up uncertain predictions to higher levels of organisation tends to underestimate change	19
aniMotum, an R package for animal movement data: Rapid quality control, behavioural estimation and simulation	19
PhycoCanopy: An R Shiny tool for exploring primary production in macroalgal canopies	19
Practical guidelines and the EMLN R package for handling ecological multilayer networks	19
Design and performance of an ecosystem‐scale forest soil warming experiment with infrared heater arrays	18
Using ensemble methods to improve the robustness of deep learning for image classification in marine environments	18
Managing risk and uncertainty in systematic conservation planning with insufficient information	18
Guidelines for the prediction of species interactions through binary classification	18
SlicerMorph: An open and extensible platform to retrieve, visualize and analyse 3D morphology	18
Scalable phylogenetic Gaussian process models improve the detectability of environmental signals on local extinctions for many Red List species	18
Methods to account for incomplete viewsheds in distance sampling	18
The Latent Dirichlet Allocation model applied to airborne LiDAR data: A case study on mapping forest degradation associated with fragmentation and fire in the Amazon region	18
Estimating interaction strengths for diverse horizontal systems using performance data	17
soundClass: An automatic sound classification tool for biodiversity monitoring using machine learning	17
A low‐cost IoT network to monitor microclimate variables in ecosystems	17
Unifying individual differences in personality, predictability and plasticity: A practical guide	17
Cover Picture and Issue Information	17
Pitfalls arising from site selection bias in population monitoring defy simple heuristics	17
starve: An R package for spatio‐temporal analysis of research survey data using nearest‐neighbour Gaussian processes	17
A GLMM approach for combining multiple relative abundance surfaces	17
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Extending isolation by resistance to predict genetic connectivity	16
Including the invisible fraction in whole population studies: A guide to the genetic sampling of unhatched bird eggs	16
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Quantifying the utilisation of blue, green and brown resources by riparian predators: A combined use of amino acid isotopes and fatty acids	16
Streamlining analysis methods for large acoustic surveys using automatic detectors with operator validation	16
Introducing the combined atlas framework for large‐scale web‐based data visualization: The GloNAF atlas of plant invasion	16
CaptuRING: A do‐it‐yourself tool for wood sample digitization	16
Hard tissue thin‐sectioning techniques in vertebrate paleohistology: Review, synthesis and improvements	16
ecochange: An R‐package to derive ecosystem change indicators from freely available earth observation products	16
allodb: An R package for biomass estimation at globally distributed extratropical forest plots	16
Acoustic and archival technologies join forces: A combination tag	16
Cover Picture and Issue Information	16
A conceptual framework for host‐associated microbiomes of hybrid organisms	16
Correction to ‘The Aquatic Metatron: A large‐scale experimental facility to study the combined effects of habitat fragmentation and climate change on aquatic meta‐ecosystems’	16
Population assignment from genotype likelihoods for low‐coverage whole‐genome sequencing data	15
A unifying framework for quantifying and comparing n‐dimensional hypervolumes	15
PiCAM: A Raspberry Pi‐based open‐source, low‐power camera system for monitoring plant phenology in Arctic environments	15
3D photogrammetry and deep‐learning deliver accurate estimates of epibenthic biomass	15
Generating continuous maps of genetic diversity using moving windows	15
Long‐term collar deployment leads to bias in soil respiration measurements	15
A framework for post‐processing bird tracks from automated tracking radar systems	15
The use of weighted averages of Hedges' d in meta‐analysis: Is it worth it?	15
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ENphylo: A new method to model the distribution of extremely rare species	15
PoolDilutionR: An R package for easy optimization of isotope pool dilution calculations	15
Real‐time alerts from AI‐enabled camera traps using the Iridium satellite network: A case‐study in Gabon, Central Africa	15
Stable isotope fingerprinting traces essential amino acid assimilation and multichannel feeding in a vertebrate consumer	15
isotracer: An R package for the analysis of tracer addition experiments	15
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Impact of acoustic index parameters on soundscape comparisons	15
Cover Picture and Issue Information	14
CATS: A high‐performance software framework for simulating plant migration in changing environments	14
ISSRseq: An extensible method for reduced representation sequencing	14
Clustering and unconstrained ordination with Dirichlet process mixture models	14
Cover Picture and Issue Information	14
The role of large language models in interdisciplinary research: Opportunities, challenges and ways forward	14
ChirpArray: A low‐cost, easy‐to‐construct microphone array for long‐term ecoacoustic monitoring	14
Analysing biodiversity observation data collected in continuous time: Should we use discrete‐ or continuous‐time occupancy models?	14
Connectivity conservation planning through deep reinforcement learning	14
Sap Flow Analyzer: A tool to standardize sap flow estimation and scaling to whole‐tree water use using the HFD method	14
TransMCL enables the assembly of full‐length coding genes for collecting complete hierarchical orthogroups	14
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rphenoscate: An R package for semantics‐aware evolutionary analyses of anatomical traits	14
Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot	14
bistro: An R package for vector bloodmeal identification by short tandem repeat overlap	13
Ten practical guidelines for microclimate research in terrestrial ecosystems	13
The geodiv r package: Tools for calculating gradient surface metrics	13
Cost‐effective seafloor habitat mapping using a portable speedy sea scanner and deep‐learning‐based segmentation: A sea trial at Pujada Bay, Philippines	13
Estimating forest above‐ground biomass with terrestrial laser scanning: Current status and future directions	13
Applying computer vision to digitised natural history collections for climate change research: Temperature‐size responses in British butterflies	13
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes	13
Broad‐scale applications of the Raspberry Pi: A review and guide for biologists	13
HemiPy: A Python module for automated estimation of forest biophysical variables and uncertainties from digital hemispherical photographs	13
Estimating animal density for a community of species using information obtained only from camera‐traps	13
A model selection approach to structural equation modelling: A critical evaluation and a road map for ecologists	13
Continuous‐surface geographic assignment of migratory animals using strontium isotopes: A case study with monarch butterflies	13
Realising the promise of large data and complex models	13
A continuous‐score occupancy model that incorporates uncertain machine learning output from autonomous biodiversity surveys	13
HSC3D: A Python package to quantify three‐dimensional habitat structural complexity	13
A heuristic method to evaluate consequences for flight control and stability induced by attachment of biologging devices to birds and bats	12
Reconstructing bird trajectories from pressure and wind data using a highly optimized hidden Markov model	12
Cover Picture and Issue Information	12
EEMtoolbox: A user‐friendly R package for flexible ensemble ecosystem modelling	12
An RGB‐D framework for capturing soft‐sediment microtopography	12
A Monte Carlo resampling framework for implementing goodness‐of‐fit tests in spatial capture‐recapture models	12
Decoding the footsteps of the African savanna: Classifying wildlife using seismic signals and machine learning	12
ontophylo: Reconstructing the evolutionary dynamics of phenomes using new ontology‐informed phylogenetic methods	12
patter: Particle algorithms for animal tracking in R and Julia	12
mpmsim: An R package for simulating matrix population models	12
plantTracker: An R package to translate maps of plant occurrence into demographic data	12
Cover Picture and Issue Information	12
metaRange: A framework to build mechanistic range models	12
A multi‐property assessment of intensity of use provides a functional understanding of animal movement	12
High‐magnification platform for characterising microscopic communities	12
Bioregionalization analyses with the bioregion R package	12
Wellcounter: Automated high‐throughput phenotyping for aquatic microinvertebrates	12
Corrigendum	12
A new tool to improve the estimates of interaction rewiring considering the whole community composition	12
BatRack: An open‐source multi‐sensor device for wildlife research	12
USE it: Uniformly sampling pseudo‐absences within the environmental space for applications in habitat suitability models	12
AMMonitor 2: Remote monitoring of biodiversity in an adaptive framework in R	12
Simple assay quantifying sediment resuspension effects on marine carbon storage	12
Deep reinforcement learning for conservation decisions	11
Introduction to deep learning methods for multi‐species predictions	11
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Impact network analysis and the ina r package: Decision support for regional management interventions	11
Avoiding confusion: Modelling image identification surveys with classification errors	11
dentist: Quantifying uncertainty by sampling points around maximum likelihood estimates	11
Cover Picture and Issue Information	11
An automated radiotelemetry system (ARTS) for monitoring small mammals	11
Method for maintaining adult solitary bee Centris analis under laboratory conditions	11
Cover Picture and Issue Information	11
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DA: Population structure inference using discriminant analysis	11
Integrating eco‐evolutionary dynamics into matrix population models for structured populations: Discrete and continuous frameworks	11
Know what you don't know: Embracing state uncertainty in disease‐structured multistate models	11
Detecting stochasticity in population time series using a non‐parametric test of intrinsic predictability	11
Fieldwork in conservation organisations–A review of methodological challenges, opportunities and ethics	11